Mercurial > repos > chemteam > gmx_check
comparison test-data/complex.top @ 0:26467f738ed4 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
author | chemteam |
---|---|
date | Tue, 12 Jul 2022 12:48:09 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:26467f738ed4 |
---|---|
1 ; | |
2 ; File 'topol.top' was generated | |
3 ; By user: unknown (1000) | |
4 ; On host: simon-notebook | |
5 ; At date: Tue May 12 12:59:21 2020 | |
6 ; | |
7 ; This is a standalone topology file | |
8 ; | |
9 ; Created by: | |
10 ; :-) GROMACS - gmx pdb2gmx, 2019.1 (-: | |
11 ; | |
12 ; Executable: /home/simon/miniconda3/envs/__gromacs@2019.1/bin/gmx | |
13 ; Data prefix: /home/simon/miniconda3/envs/__gromacs@2019.1 | |
14 ; Working dir: /tmp/tmpg0ncnt9q/job_working_directory/000/10/working | |
15 ; Command line: | |
16 ; gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all | |
17 ; Force field was read from the standard GROMACS share directory. | |
18 ; | |
19 | |
20 ; Include forcefield parameters | |
21 #include "oplsaa.ff/forcefield.itp" | |
22 | |
23 ; Include ligand atomtypes | |
24 [ atomtypes ] | |
25 ;name bond_type mass charge ptype sigma epsilon Amb | |
26 C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 | |
27 CZ CZ 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 | |
28 CK CK 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 | |
29 CM CM 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 | |
30 CD CD 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 | |
31 NB NB 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 | |
32 N* N* 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 | |
33 DU DU 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000 | |
34 F F 0.00000 0.00000 A 3.11815e-01 2.55224e-01 ; 1.75 0.0610 | |
35 O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 | |
36 | |
37 [ moleculetype ] | |
38 ; Name nrexcl | |
39 Protein 3 | |
40 | |
41 [ atoms ] | |
42 ; nr type resnr residue atom cgnr charge mass typeB chargeB massB | |
43 ; residue 1 LYS rtp LYSH q +2.0 | |
44 1 opls_287 1 LYS N 1 -0.3 14.0027 | |
45 2 opls_290 1 LYS H1 1 0.33 1.008 | |
46 3 opls_290 1 LYS H2 1 0.33 1.008 | |
47 4 opls_290 1 LYS H3 1 0.33 1.008 | |
48 5 opls_293B 1 LYS CA 1 0.25 12.011 | |
49 6 opls_140 1 LYS HA 1 0.06 1.008 | |
50 7 opls_136 1 LYS CB 2 -0.12 12.011 | |
51 8 opls_140 1 LYS HB1 2 0.06 1.008 | |
52 9 opls_140 1 LYS HB2 2 0.06 1.008 | |
53 10 opls_136 1 LYS CG 3 -0.12 12.011 | |
54 11 opls_140 1 LYS HG1 3 0.06 1.008 | |
55 12 opls_140 1 LYS HG2 3 0.06 1.008 | |
56 13 opls_136 1 LYS CD 4 -0.12 12.011 | |
57 14 opls_140 1 LYS HD1 4 0.06 1.008 | |
58 15 opls_140 1 LYS HD2 4 0.06 1.008 | |
59 16 opls_292 1 LYS CE 5 0.19 12.011 | |
60 17 opls_140 1 LYS HE1 5 0.06 1.008 | |
61 18 opls_140 1 LYS HE2 5 0.06 1.008 | |
62 19 opls_287 1 LYS NZ 6 -0.3 14.0067 | |
63 20 opls_290 1 LYS HZ1 6 0.33 1.008 | |
64 21 opls_290 1 LYS HZ2 6 0.33 1.008 | |
65 22 opls_290 1 LYS HZ3 6 0.33 1.008 | |
66 23 opls_235 1 LYS C 7 0.5 12.011 | |
67 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2 | |
68 ; residue 2 VAL rtp VAL q 0.0 | |
69 25 opls_238 2 VAL N 8 -0.5 14.0067 | |
70 26 opls_241 2 VAL H 8 0.3 1.008 | |
71 27 opls_224B 2 VAL CA 8 0.14 12.011 | |
72 28 opls_140 2 VAL HA 8 0.06 1.008 | |
73 29 opls_137 2 VAL CB 9 -0.06 12.011 | |
74 30 opls_140 2 VAL HB 9 0.06 1.008 | |
75 31 opls_135 2 VAL CG1 10 -0.18 12.011 | |
76 32 opls_140 2 VAL HG11 10 0.06 1.008 | |
77 33 opls_140 2 VAL HG12 10 0.06 1.008 | |
78 34 opls_140 2 VAL HG13 10 0.06 1.008 | |
79 35 opls_135 2 VAL CG2 11 -0.18 12.011 | |
80 36 opls_140 2 VAL HG21 11 0.06 1.008 | |
81 37 opls_140 2 VAL HG22 11 0.06 1.008 | |
82 38 opls_140 2 VAL HG23 11 0.06 1.008 | |
83 39 opls_235 2 VAL C 12 0.5 12.011 | |
84 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2 | |
85 ; residue 3 PHE rtp PHE q 0.0 | |
86 41 opls_238 3 PHE N 13 -0.5 14.0067 | |
87 42 opls_241 3 PHE H 13 0.3 1.008 | |
88 43 opls_224B 3 PHE CA 13 0.14 12.011 | |
89 44 opls_140 3 PHE HA 13 0.06 1.008 | |
90 45 opls_149 3 PHE CB 14 -0.005 12.011 | |
91 46 opls_140 3 PHE HB1 14 0.06 1.008 | |
92 47 opls_140 3 PHE HB2 14 0.06 1.008 | |
93 48 opls_145 3 PHE CG 14 -0.115 12.011 | |
94 49 opls_145 3 PHE CD1 15 -0.115 12.011 | |
95 50 opls_146 3 PHE HD1 15 0.115 1.008 | |
96 51 opls_145 3 PHE CD2 16 -0.115 12.011 | |
97 52 opls_146 3 PHE HD2 16 0.115 1.008 | |
98 53 opls_145 3 PHE CE1 17 -0.115 12.011 | |
99 54 opls_146 3 PHE HE1 17 0.115 1.008 | |
100 55 opls_145 3 PHE CE2 18 -0.115 12.011 | |
101 56 opls_146 3 PHE HE2 18 0.115 1.008 | |
102 57 opls_145 3 PHE CZ 19 -0.115 12.011 | |
103 58 opls_146 3 PHE HZ 19 0.115 1.008 | |
104 59 opls_235 3 PHE C 20 0.5 12.011 | |
105 60 opls_236 3 PHE O 20 -0.5 15.9994 ; qtot 2 | |
106 ; residue 4 GLY rtp GLY q 0.0 | |
107 61 opls_238 4 GLY N 21 -0.5 14.0067 | |
108 62 opls_241 4 GLY H 21 0.3 1.008 | |
109 63 opls_223B 4 GLY CA 21 0.08 12.011 | |
110 64 opls_140 4 GLY HA1 21 0.06 1.008 | |
111 65 opls_140 4 GLY HA2 21 0.06 1.008 | |
112 66 opls_235 4 GLY C 22 0.5 12.011 | |
113 67 opls_236 4 GLY O 22 -0.5 15.9994 ; qtot 2 | |
114 ; residue 5 ARG rtp ARG q 0.0 | |
115 68 opls_238 5 ARG N 23 -0.5 14.0067 | |
116 69 opls_241 5 ARG H 23 0.3 1.008 | |
117 70 opls_283 5 ARG CA 23 0.04 12.011 | |
118 71 opls_140 5 ARG HA 23 0.06 1.008 | |
119 72 opls_136 5 ARG CB 24 -0.12 12.011 | |
120 73 opls_140 5 ARG HB1 24 0.06 1.008 | |
121 74 opls_140 5 ARG HB2 24 0.06 1.008 | |
122 75 opls_308 5 ARG CG 25 -0.05 12.011 | |
123 76 opls_140 5 ARG HG1 25 0.06 1.008 | |
124 77 opls_140 5 ARG HG2 25 0.06 1.008 | |
125 78 opls_307 5 ARG CD 26 0.19 12.011 | |
126 79 opls_140 5 ARG HD1 26 0.06 1.008 | |
127 80 opls_140 5 ARG HD2 26 0.06 1.008 | |
128 81 opls_303 5 ARG NE 27 -0.7 14.0067 | |
129 82 opls_304 5 ARG HE 27 0.44 1.008 | |
130 83 opls_302 5 ARG CZ 27 0.64 12.011 | |
131 84 opls_300 5 ARG NH1 28 -0.8 14.0067 | |
132 85 opls_301 5 ARG HH11 28 0.46 1.008 | |
133 86 opls_301 5 ARG HH12 28 0.46 1.008 | |
134 87 opls_300 5 ARG NH2 29 -0.8 14.0067 | |
135 88 opls_301 5 ARG HH21 29 0.46 1.008 | |
136 89 opls_301 5 ARG HH22 29 0.46 1.008 | |
137 90 opls_271 5 ARG C 30 0.7 12.011 | |
138 91 opls_272 5 ARG O1 30 -0.8 15.9994 | |
139 92 opls_272 5 ARG O2 30 -0.8 15.9994 ; qtot 2 | |
140 | |
141 [ bonds ] | |
142 ; ai aj funct c0 c1 c2 c3 | |
143 1 2 1 | |
144 1 3 1 | |
145 1 4 1 | |
146 1 5 1 | |
147 5 6 1 | |
148 5 7 1 | |
149 5 23 1 | |
150 7 8 1 | |
151 7 9 1 | |
152 7 10 1 | |
153 10 11 1 | |
154 10 12 1 | |
155 10 13 1 | |
156 13 14 1 | |
157 13 15 1 | |
158 13 16 1 | |
159 16 17 1 | |
160 16 18 1 | |
161 16 19 1 | |
162 19 20 1 | |
163 19 21 1 | |
164 19 22 1 | |
165 23 24 1 | |
166 23 25 1 | |
167 25 26 1 | |
168 25 27 1 | |
169 27 28 1 | |
170 27 29 1 | |
171 27 39 1 | |
172 29 30 1 | |
173 29 31 1 | |
174 29 35 1 | |
175 31 32 1 | |
176 31 33 1 | |
177 31 34 1 | |
178 35 36 1 | |
179 35 37 1 | |
180 35 38 1 | |
181 39 40 1 | |
182 39 41 1 | |
183 41 42 1 | |
184 41 43 1 | |
185 43 44 1 | |
186 43 45 1 | |
187 43 59 1 | |
188 45 46 1 | |
189 45 47 1 | |
190 45 48 1 | |
191 48 49 1 | |
192 48 51 1 | |
193 49 50 1 | |
194 49 53 1 | |
195 51 52 1 | |
196 51 55 1 | |
197 53 54 1 | |
198 53 57 1 | |
199 55 56 1 | |
200 55 57 1 | |
201 57 58 1 | |
202 59 60 1 | |
203 59 61 1 | |
204 61 62 1 | |
205 61 63 1 | |
206 63 64 1 | |
207 63 65 1 | |
208 63 66 1 | |
209 66 67 1 | |
210 66 68 1 | |
211 68 69 1 | |
212 68 70 1 | |
213 70 71 1 | |
214 70 72 1 | |
215 70 90 1 | |
216 72 73 1 | |
217 72 74 1 | |
218 72 75 1 | |
219 75 76 1 | |
220 75 77 1 | |
221 75 78 1 | |
222 78 79 1 | |
223 78 80 1 | |
224 78 81 1 | |
225 81 82 1 | |
226 81 83 1 | |
227 83 84 1 | |
228 83 87 1 | |
229 84 85 1 | |
230 84 86 1 | |
231 87 88 1 | |
232 87 89 1 | |
233 90 91 1 | |
234 90 92 1 | |
235 | |
236 [ pairs ] | |
237 ; ai aj funct c0 c1 c2 c3 | |
238 1 8 1 | |
239 1 9 1 | |
240 1 10 1 | |
241 1 24 1 | |
242 1 25 1 | |
243 2 6 1 | |
244 2 7 1 | |
245 2 23 1 | |
246 3 6 1 | |
247 3 7 1 | |
248 3 23 1 | |
249 4 6 1 | |
250 4 7 1 | |
251 4 23 1 | |
252 5 11 1 | |
253 5 12 1 | |
254 5 13 1 | |
255 5 26 1 | |
256 5 27 1 | |
257 6 8 1 | |
258 6 9 1 | |
259 6 10 1 | |
260 6 24 1 | |
261 6 25 1 | |
262 7 14 1 | |
263 7 15 1 | |
264 7 16 1 | |
265 7 24 1 | |
266 7 25 1 | |
267 8 11 1 | |
268 8 12 1 | |
269 8 13 1 | |
270 8 23 1 | |
271 9 11 1 | |
272 9 12 1 | |
273 9 13 1 | |
274 9 23 1 | |
275 10 17 1 | |
276 10 18 1 | |
277 10 19 1 | |
278 10 23 1 | |
279 11 14 1 | |
280 11 15 1 | |
281 11 16 1 | |
282 12 14 1 | |
283 12 15 1 | |
284 12 16 1 | |
285 13 20 1 | |
286 13 21 1 | |
287 13 22 1 | |
288 14 17 1 | |
289 14 18 1 | |
290 14 19 1 | |
291 15 17 1 | |
292 15 18 1 | |
293 15 19 1 | |
294 17 20 1 | |
295 17 21 1 | |
296 17 22 1 | |
297 18 20 1 | |
298 18 21 1 | |
299 18 22 1 | |
300 23 28 1 | |
301 23 29 1 | |
302 23 39 1 | |
303 24 26 1 | |
304 24 27 1 | |
305 25 30 1 | |
306 25 31 1 | |
307 25 35 1 | |
308 25 40 1 | |
309 25 41 1 | |
310 26 28 1 | |
311 26 29 1 | |
312 26 39 1 | |
313 27 32 1 | |
314 27 33 1 | |
315 27 34 1 | |
316 27 36 1 | |
317 27 37 1 | |
318 27 38 1 | |
319 27 42 1 | |
320 27 43 1 | |
321 28 30 1 | |
322 28 31 1 | |
323 28 35 1 | |
324 28 40 1 | |
325 28 41 1 | |
326 29 40 1 | |
327 29 41 1 | |
328 30 32 1 | |
329 30 33 1 | |
330 30 34 1 | |
331 30 36 1 | |
332 30 37 1 | |
333 30 38 1 | |
334 30 39 1 | |
335 31 36 1 | |
336 31 37 1 | |
337 31 38 1 | |
338 31 39 1 | |
339 32 35 1 | |
340 33 35 1 | |
341 34 35 1 | |
342 35 39 1 | |
343 39 44 1 | |
344 39 45 1 | |
345 39 59 1 | |
346 40 42 1 | |
347 40 43 1 | |
348 41 46 1 | |
349 41 47 1 | |
350 41 48 1 | |
351 41 60 1 | |
352 41 61 1 | |
353 42 44 1 | |
354 42 45 1 | |
355 42 59 1 | |
356 43 49 1 | |
357 43 51 1 | |
358 43 62 1 | |
359 43 63 1 | |
360 44 46 1 | |
361 44 47 1 | |
362 44 48 1 | |
363 44 60 1 | |
364 44 61 1 | |
365 45 50 1 | |
366 45 52 1 | |
367 45 53 1 | |
368 45 55 1 | |
369 45 60 1 | |
370 45 61 1 | |
371 46 49 1 | |
372 46 51 1 | |
373 46 59 1 | |
374 47 49 1 | |
375 47 51 1 | |
376 47 59 1 | |
377 48 54 1 | |
378 48 56 1 | |
379 48 57 1 | |
380 48 59 1 | |
381 49 52 1 | |
382 49 55 1 | |
383 49 58 1 | |
384 50 51 1 | |
385 50 54 1 | |
386 50 57 1 | |
387 51 53 1 | |
388 51 58 1 | |
389 52 56 1 | |
390 52 57 1 | |
391 53 56 1 | |
392 54 55 1 | |
393 54 58 1 | |
394 56 58 1 | |
395 59 64 1 | |
396 59 65 1 | |
397 59 66 1 | |
398 60 62 1 | |
399 60 63 1 | |
400 61 67 1 | |
401 61 68 1 | |
402 62 64 1 | |
403 62 65 1 | |
404 62 66 1 | |
405 63 69 1 | |
406 63 70 1 | |
407 64 67 1 | |
408 64 68 1 | |
409 65 67 1 | |
410 65 68 1 | |
411 66 71 1 | |
412 66 72 1 | |
413 66 90 1 | |
414 67 69 1 | |
415 67 70 1 | |
416 68 73 1 | |
417 68 74 1 | |
418 68 75 1 | |
419 68 91 1 | |
420 68 92 1 | |
421 69 71 1 | |
422 69 72 1 | |
423 69 90 1 | |
424 70 76 1 | |
425 70 77 1 | |
426 70 78 1 | |
427 71 73 1 | |
428 71 74 1 | |
429 71 75 1 | |
430 71 91 1 | |
431 71 92 1 | |
432 72 79 1 | |
433 72 80 1 | |
434 72 81 1 | |
435 72 91 1 | |
436 72 92 1 | |
437 73 76 1 | |
438 73 77 1 | |
439 73 78 1 | |
440 73 90 1 | |
441 74 76 1 | |
442 74 77 1 | |
443 74 78 1 | |
444 74 90 1 | |
445 75 82 1 | |
446 75 83 1 | |
447 75 90 1 | |
448 76 79 1 | |
449 76 80 1 | |
450 76 81 1 | |
451 77 79 1 | |
452 77 80 1 | |
453 77 81 1 | |
454 78 84 1 | |
455 78 87 1 | |
456 79 82 1 | |
457 79 83 1 | |
458 80 82 1 | |
459 80 83 1 | |
460 81 85 1 | |
461 81 86 1 | |
462 81 88 1 | |
463 81 89 1 | |
464 82 84 1 | |
465 82 87 1 | |
466 84 88 1 | |
467 84 89 1 | |
468 85 87 1 | |
469 86 87 1 | |
470 | |
471 [ angles ] | |
472 ; ai aj ak funct c0 c1 c2 c3 | |
473 2 1 3 1 | |
474 2 1 4 1 | |
475 2 1 5 1 | |
476 3 1 4 1 | |
477 3 1 5 1 | |
478 4 1 5 1 | |
479 1 5 6 1 | |
480 1 5 7 1 | |
481 1 5 23 1 | |
482 6 5 7 1 | |
483 6 5 23 1 | |
484 7 5 23 1 | |
485 5 7 8 1 | |
486 5 7 9 1 | |
487 5 7 10 1 | |
488 8 7 9 1 | |
489 8 7 10 1 | |
490 9 7 10 1 | |
491 7 10 11 1 | |
492 7 10 12 1 | |
493 7 10 13 1 | |
494 11 10 12 1 | |
495 11 10 13 1 | |
496 12 10 13 1 | |
497 10 13 14 1 | |
498 10 13 15 1 | |
499 10 13 16 1 | |
500 14 13 15 1 | |
501 14 13 16 1 | |
502 15 13 16 1 | |
503 13 16 17 1 | |
504 13 16 18 1 | |
505 13 16 19 1 | |
506 17 16 18 1 | |
507 17 16 19 1 | |
508 18 16 19 1 | |
509 16 19 20 1 | |
510 16 19 21 1 | |
511 16 19 22 1 | |
512 20 19 21 1 | |
513 20 19 22 1 | |
514 21 19 22 1 | |
515 5 23 24 1 | |
516 5 23 25 1 | |
517 24 23 25 1 | |
518 23 25 26 1 | |
519 23 25 27 1 | |
520 26 25 27 1 | |
521 25 27 28 1 | |
522 25 27 29 1 | |
523 25 27 39 1 | |
524 28 27 29 1 | |
525 28 27 39 1 | |
526 29 27 39 1 | |
527 27 29 30 1 | |
528 27 29 31 1 | |
529 27 29 35 1 | |
530 30 29 31 1 | |
531 30 29 35 1 | |
532 31 29 35 1 | |
533 29 31 32 1 | |
534 29 31 33 1 | |
535 29 31 34 1 | |
536 32 31 33 1 | |
537 32 31 34 1 | |
538 33 31 34 1 | |
539 29 35 36 1 | |
540 29 35 37 1 | |
541 29 35 38 1 | |
542 36 35 37 1 | |
543 36 35 38 1 | |
544 37 35 38 1 | |
545 27 39 40 1 | |
546 27 39 41 1 | |
547 40 39 41 1 | |
548 39 41 42 1 | |
549 39 41 43 1 | |
550 42 41 43 1 | |
551 41 43 44 1 | |
552 41 43 45 1 | |
553 41 43 59 1 | |
554 44 43 45 1 | |
555 44 43 59 1 | |
556 45 43 59 1 | |
557 43 45 46 1 | |
558 43 45 47 1 | |
559 43 45 48 1 | |
560 46 45 47 1 | |
561 46 45 48 1 | |
562 47 45 48 1 | |
563 45 48 49 1 | |
564 45 48 51 1 | |
565 49 48 51 1 | |
566 48 49 50 1 | |
567 48 49 53 1 | |
568 50 49 53 1 | |
569 48 51 52 1 | |
570 48 51 55 1 | |
571 52 51 55 1 | |
572 49 53 54 1 | |
573 49 53 57 1 | |
574 54 53 57 1 | |
575 51 55 56 1 | |
576 51 55 57 1 | |
577 56 55 57 1 | |
578 53 57 55 1 | |
579 53 57 58 1 | |
580 55 57 58 1 | |
581 43 59 60 1 | |
582 43 59 61 1 | |
583 60 59 61 1 | |
584 59 61 62 1 | |
585 59 61 63 1 | |
586 62 61 63 1 | |
587 61 63 64 1 | |
588 61 63 65 1 | |
589 61 63 66 1 | |
590 64 63 65 1 | |
591 64 63 66 1 | |
592 65 63 66 1 | |
593 63 66 67 1 | |
594 63 66 68 1 | |
595 67 66 68 1 | |
596 66 68 69 1 | |
597 66 68 70 1 | |
598 69 68 70 1 | |
599 68 70 71 1 | |
600 68 70 72 1 | |
601 68 70 90 1 | |
602 71 70 72 1 | |
603 71 70 90 1 | |
604 72 70 90 1 | |
605 70 72 73 1 | |
606 70 72 74 1 | |
607 70 72 75 1 | |
608 73 72 74 1 | |
609 73 72 75 1 | |
610 74 72 75 1 | |
611 72 75 76 1 | |
612 72 75 77 1 | |
613 72 75 78 1 | |
614 76 75 77 1 | |
615 76 75 78 1 | |
616 77 75 78 1 | |
617 75 78 79 1 | |
618 75 78 80 1 | |
619 75 78 81 1 | |
620 79 78 80 1 | |
621 79 78 81 1 | |
622 80 78 81 1 | |
623 78 81 82 1 | |
624 78 81 83 1 | |
625 82 81 83 1 | |
626 81 83 84 1 | |
627 81 83 87 1 | |
628 84 83 87 1 | |
629 83 84 85 1 | |
630 83 84 86 1 | |
631 85 84 86 1 | |
632 83 87 88 1 | |
633 83 87 89 1 | |
634 88 87 89 1 | |
635 70 90 91 1 | |
636 70 90 92 1 | |
637 91 90 92 1 | |
638 | |
639 [ dihedrals ] | |
640 ; ai aj ak al funct c0 c1 c2 c3 c4 c5 | |
641 2 1 5 6 3 | |
642 2 1 5 7 3 | |
643 2 1 5 23 3 | |
644 3 1 5 6 3 | |
645 3 1 5 7 3 | |
646 3 1 5 23 3 | |
647 4 1 5 6 3 | |
648 4 1 5 7 3 | |
649 4 1 5 23 3 | |
650 1 5 7 10 3 dih_LYS_chi1_N_C_C_C | |
651 23 5 7 10 3 dih_LYS_chi1_C_C_C_CO | |
652 1 5 7 8 3 | |
653 1 5 7 9 3 | |
654 6 5 7 8 3 | |
655 6 5 7 9 3 | |
656 6 5 7 10 3 | |
657 23 5 7 8 3 | |
658 23 5 7 9 3 | |
659 1 5 23 24 3 | |
660 1 5 23 25 3 | |
661 6 5 23 24 3 | |
662 6 5 23 25 3 | |
663 7 5 23 24 3 | |
664 7 5 23 25 3 | |
665 5 7 10 11 3 | |
666 5 7 10 12 3 | |
667 5 7 10 13 3 | |
668 8 7 10 11 3 | |
669 8 7 10 12 3 | |
670 8 7 10 13 3 | |
671 9 7 10 11 3 | |
672 9 7 10 12 3 | |
673 9 7 10 13 3 | |
674 7 10 13 14 3 | |
675 7 10 13 15 3 | |
676 7 10 13 16 3 | |
677 11 10 13 14 3 | |
678 11 10 13 15 3 | |
679 11 10 13 16 3 | |
680 12 10 13 14 3 | |
681 12 10 13 15 3 | |
682 12 10 13 16 3 | |
683 10 13 16 17 3 | |
684 10 13 16 18 3 | |
685 10 13 16 19 3 | |
686 14 13 16 17 3 | |
687 14 13 16 18 3 | |
688 14 13 16 19 3 | |
689 15 13 16 17 3 | |
690 15 13 16 18 3 | |
691 15 13 16 19 3 | |
692 13 16 19 20 3 dih_LYS_chi5_C_C_N_H | |
693 13 16 19 21 3 dih_LYS_chi5_C_C_N_H | |
694 13 16 19 22 3 dih_LYS_chi5_C_C_N_H | |
695 17 16 19 20 3 | |
696 17 16 19 21 3 | |
697 17 16 19 22 3 | |
698 18 16 19 20 3 | |
699 18 16 19 21 3 | |
700 18 16 19 22 3 | |
701 5 23 25 26 3 | |
702 5 23 25 27 3 | |
703 24 23 25 26 3 | |
704 24 23 25 27 3 | |
705 23 25 27 28 3 | |
706 23 25 27 29 3 | |
707 23 25 27 39 3 | |
708 26 25 27 28 3 | |
709 26 25 27 29 3 | |
710 26 25 27 39 3 | |
711 25 27 29 31 3 dih_VAL_chi1_N_C_C_C | |
712 25 27 29 35 3 dih_VAL_chi1_N_C_C_C | |
713 39 27 29 31 3 dih_VAL_chi1_C_C_C_CO | |
714 39 27 29 35 3 dih_VAL_chi1_C_C_C_CO | |
715 25 27 29 30 3 | |
716 28 27 29 30 3 | |
717 28 27 29 31 3 | |
718 28 27 29 35 3 | |
719 39 27 29 30 3 | |
720 25 27 39 40 3 | |
721 25 27 39 41 3 | |
722 28 27 39 40 3 | |
723 28 27 39 41 3 | |
724 29 27 39 40 3 | |
725 29 27 39 41 3 | |
726 27 29 31 32 3 | |
727 27 29 31 33 3 | |
728 27 29 31 34 3 | |
729 30 29 31 32 3 | |
730 30 29 31 33 3 | |
731 30 29 31 34 3 | |
732 35 29 31 32 3 | |
733 35 29 31 33 3 | |
734 35 29 31 34 3 | |
735 27 29 35 36 3 | |
736 27 29 35 37 3 | |
737 27 29 35 38 3 | |
738 30 29 35 36 3 | |
739 30 29 35 37 3 | |
740 30 29 35 38 3 | |
741 31 29 35 36 3 | |
742 31 29 35 37 3 | |
743 31 29 35 38 3 | |
744 27 39 41 42 3 | |
745 27 39 41 43 3 | |
746 40 39 41 42 3 | |
747 40 39 41 43 3 | |
748 39 41 43 44 3 | |
749 39 41 43 45 3 | |
750 39 41 43 59 3 | |
751 42 41 43 44 3 | |
752 42 41 43 45 3 | |
753 42 41 43 59 3 | |
754 41 43 45 46 3 | |
755 41 43 45 47 3 | |
756 41 43 45 48 3 | |
757 44 43 45 46 3 | |
758 44 43 45 47 3 | |
759 44 43 45 48 3 | |
760 59 43 45 46 3 | |
761 59 43 45 47 3 | |
762 59 43 45 48 3 | |
763 41 43 59 60 3 | |
764 41 43 59 61 3 | |
765 44 43 59 60 3 | |
766 44 43 59 61 3 | |
767 45 43 59 60 3 | |
768 45 43 59 61 3 | |
769 43 45 48 49 3 | |
770 43 45 48 51 3 | |
771 46 45 48 49 3 | |
772 46 45 48 51 3 | |
773 47 45 48 49 3 | |
774 47 45 48 51 3 | |
775 45 48 49 50 3 | |
776 45 48 49 53 3 | |
777 51 48 49 50 3 | |
778 51 48 49 53 3 | |
779 45 48 51 52 3 | |
780 45 48 51 55 3 | |
781 49 48 51 52 3 | |
782 49 48 51 55 3 | |
783 48 49 53 54 3 | |
784 48 49 53 57 3 | |
785 50 49 53 54 3 | |
786 50 49 53 57 3 | |
787 48 51 55 56 3 | |
788 48 51 55 57 3 | |
789 52 51 55 56 3 | |
790 52 51 55 57 3 | |
791 49 53 57 55 3 | |
792 49 53 57 58 3 | |
793 54 53 57 55 3 | |
794 54 53 57 58 3 | |
795 51 55 57 53 3 | |
796 51 55 57 58 3 | |
797 56 55 57 53 3 | |
798 56 55 57 58 3 | |
799 43 59 61 62 3 | |
800 43 59 61 63 3 | |
801 60 59 61 62 3 | |
802 60 59 61 63 3 | |
803 59 61 63 64 3 | |
804 59 61 63 65 3 | |
805 59 61 63 66 3 | |
806 62 61 63 64 3 | |
807 62 61 63 65 3 | |
808 62 61 63 66 3 | |
809 61 63 66 67 3 | |
810 61 63 66 68 3 | |
811 64 63 66 67 3 | |
812 64 63 66 68 3 | |
813 65 63 66 67 3 | |
814 65 63 66 68 3 | |
815 63 66 68 69 3 | |
816 63 66 68 70 3 | |
817 67 66 68 69 3 | |
818 67 66 68 70 3 | |
819 66 68 70 71 3 | |
820 66 68 70 72 3 | |
821 66 68 70 90 3 | |
822 69 68 70 71 3 | |
823 69 68 70 72 3 | |
824 69 68 70 90 3 | |
825 68 70 72 75 3 dih_ARG_chi1_N_C_C_C | |
826 90 70 72 75 3 dih_ARG_chi1_C_C_C_CO | |
827 68 70 72 73 3 | |
828 68 70 72 74 3 | |
829 71 70 72 73 3 | |
830 71 70 72 74 3 | |
831 71 70 72 75 3 | |
832 90 70 72 73 3 | |
833 90 70 72 74 3 | |
834 68 70 90 91 3 | |
835 68 70 90 92 3 | |
836 71 70 90 91 3 | |
837 71 70 90 92 3 | |
838 72 70 90 91 3 | |
839 72 70 90 92 3 | |
840 70 72 75 76 3 | |
841 70 72 75 77 3 | |
842 70 72 75 78 3 | |
843 73 72 75 76 3 | |
844 73 72 75 77 3 | |
845 73 72 75 78 3 | |
846 74 72 75 76 3 | |
847 74 72 75 77 3 | |
848 74 72 75 78 3 | |
849 72 75 78 79 3 | |
850 72 75 78 80 3 | |
851 72 75 78 81 3 | |
852 76 75 78 79 3 | |
853 76 75 78 80 3 | |
854 76 75 78 81 3 | |
855 77 75 78 79 3 | |
856 77 75 78 80 3 | |
857 77 75 78 81 3 | |
858 75 78 81 82 3 | |
859 75 78 81 83 3 | |
860 79 78 81 82 3 | |
861 79 78 81 83 3 | |
862 80 78 81 82 3 | |
863 80 78 81 83 3 | |
864 78 81 83 84 3 | |
865 78 81 83 87 3 | |
866 82 81 83 84 3 | |
867 82 81 83 87 3 | |
868 81 83 84 85 3 | |
869 81 83 84 86 3 | |
870 87 83 84 85 3 | |
871 87 83 84 86 3 | |
872 81 83 87 88 3 | |
873 81 83 87 89 3 | |
874 84 83 87 88 3 | |
875 84 83 87 89 3 | |
876 | |
877 [ dihedrals ] | |
878 ; ai aj ak al funct c0 c1 c2 c3 | |
879 5 25 23 24 1 improper_O_C_X_Y | |
880 23 27 25 26 1 improper_Z_N_X_Y | |
881 27 41 39 40 1 improper_O_C_X_Y | |
882 39 43 41 42 1 improper_Z_N_X_Y | |
883 43 61 59 60 1 improper_O_C_X_Y | |
884 45 48 51 49 1 improper_Z_CA_X_Y | |
885 48 53 49 50 1 improper_Z_CA_X_Y | |
886 48 55 51 52 1 improper_Z_CA_X_Y | |
887 49 57 53 54 1 improper_Z_CA_X_Y | |
888 51 57 55 56 1 improper_Z_CA_X_Y | |
889 53 55 57 58 1 improper_Z_CA_X_Y | |
890 59 63 61 62 1 improper_Z_N_X_Y | |
891 63 68 66 67 1 improper_O_C_X_Y | |
892 66 70 68 69 1 improper_Z_N_X_Y | |
893 70 91 90 92 1 improper_O_C_X_Y | |
894 78 83 81 82 1 improper_Z_N_X_Y | |
895 81 84 83 87 1 improper_O_C_X_Y | |
896 83 85 84 86 1 improper_Z_N_X_Y | |
897 83 88 87 89 1 improper_Z_N_X_Y | |
898 | |
899 ; Include Position restraint file | |
900 #ifdef POSRES | |
901 #include "posres.itp" | |
902 #endif | |
903 | |
904 ; Include ligand topology | |
905 ; base_GMX.itp created by acpype (v: 2019-11-07T23:16:00CET) on Fri Mar 20 14:38:01 2020 | |
906 | |
907 [ moleculetype ] | |
908 ;name nrexcl | |
909 base 3 | |
910 | |
911 [ atoms ] | |
912 ; nr type resi res atom cgnr charge mass ; qtot bond_type | |
913 1 C 1 G5E C1 1 0.545501 12.01000 ; qtot 0.546 | |
914 2 CZ 1 G5E C2 2 0.075000 12.01000 ; qtot 0.621 | |
915 3 C 1 G5E C3 3 0.508501 12.01000 ; qtot 1.129 | |
916 4 CK 1 G5E C7 4 0.208200 12.01000 ; qtot 1.337 | |
917 5 C 1 G5E C10 5 0.352800 12.01000 ; qtot 1.690 | |
918 6 CM 1 G5E C12 6 0.002500 12.01000 ; qtot 1.693 | |
919 7 CM 1 G5E C13 7 0.233400 12.01000 ; qtot 1.926 | |
920 8 CZ 1 G5E C14 8 -0.087900 12.01000 ; qtot 1.838 | |
921 9 CZ 1 G5E C15 9 0.072000 12.01000 ; qtot 1.910 | |
922 10 CZ 1 G5E C16 10 0.028000 12.01000 ; qtot 1.938 | |
923 11 CD 1 G5E C4 11 -0.048900 12.01000 ; qtot 1.889 | |
924 12 CZ 1 G5E C5 12 -0.123300 12.01000 ; qtot 1.766 | |
925 13 CZ 1 G5E C6 13 -0.161200 12.01000 ; qtot 1.605 | |
926 14 NB 1 G5E N8 14 -0.082600 14.01000 ; qtot 1.522 | |
927 15 NB 1 G5E N9 15 -0.125400 14.01000 ; qtot 1.397 | |
928 16 N* 1 G5E N11 16 -0.261200 14.01000 ; qtot 1.135 | |
929 17 CZ 1 G5E C17 17 -0.043900 12.01000 ; qtot 1.092 | |
930 18 DU 1 G5E S18 18 -0.081400 0.00000 ; qtot 1.010 | |
931 19 F 1 G5E F19 19 -0.100500 19.00000 ; qtot 0.910 | |
932 20 O 1 G5E O20 20 -0.460300 16.00000 ; qtot 0.449 | |
933 21 O 1 G5E O21 21 -0.449300 16.00000 ; qtot -0.000 | |
934 | |
935 [ bonds ] | |
936 ; ai aj funct r k | |
937 1 2 1 1.4600e-01 3.1782e+05 ; C1 - C2 | |
938 1 13 1 1.4600e-01 3.1782e+05 ; C1 - C6 | |
939 1 21 1 1.2290e-01 4.7698e+05 ; C1 - O21 | |
940 2 3 1 1.4600e-01 3.1782e+05 ; C2 - C3 | |
941 3 11 1 1.4680e-01 3.1045e+05 ; C3 - C4 | |
942 3 20 1 1.2290e-01 4.7698e+05 ; C3 - O20 | |
943 4 11 1 1.4280e-01 3.5129e+05 ; C7 - C4 | |
944 4 14 1 1.3040e-01 4.4267e+05 ; C7 - N8 | |
945 4 16 1 1.3710e-01 3.6819e+05 ; C7 - N11 | |
946 5 15 1 1.3870e-01 3.4886e+05 ; C10 - N9 | |
947 5 16 1 1.3830e-01 3.5480e+05 ; C10 - N11 | |
948 5 18 1 0.0000e+00 0.0000e+00 ; C10 - S18 | |
949 6 7 1 1.3500e-01 4.5940e+05 ; C12 - C13 | |
950 6 16 1 1.3650e-01 3.7489e+05 ; C12 - N11 | |
951 6 17 1 1.4400e-01 3.3815e+05 ; C12 - C17 | |
952 7 8 1 1.4400e-01 3.3815e+05 ; C13 - C14 | |
953 7 19 1 1.3490e-01 2.9941e+05 ; C13 - F19 | |
954 8 9 1 1.2060e-01 5.0208e+05 ; C14 - C15 | |
955 9 10 1 1.2060e-01 5.0208e+05 ; C15 - C16 | |
956 10 17 1 1.2060e-01 5.0208e+05 ; C16 - C17 | |
957 11 12 1 1.3150e-01 5.0827e+05 ; C4 - C5 | |
958 12 13 1 1.2060e-01 5.0208e+05 ; C5 - C6 | |
959 14 15 1 1.3650e-01 4.2710e+05 ; N8 - N9 | |
960 | |
961 [ pairs ] | |
962 ; ai aj funct | |
963 1 11 1 ; C1 - C4 | |
964 1 20 1 ; C1 - O20 | |
965 2 4 1 ; C2 - C7 | |
966 2 12 1 ; C2 - C5 | |
967 3 13 1 ; C3 - C6 | |
968 3 14 1 ; C3 - N8 | |
969 3 16 1 ; C3 - N11 | |
970 4 7 1 ; C7 - C13 | |
971 4 13 1 ; C7 - C6 | |
972 4 17 1 ; C7 - C17 | |
973 4 18 1 ; C7 - S18 | |
974 4 20 1 ; C7 - O20 | |
975 5 7 1 ; C10 - C13 | |
976 5 11 1 ; C10 - C4 | |
977 5 17 1 ; C10 - C17 | |
978 6 9 1 ; C12 - C15 | |
979 6 11 1 ; C12 - C4 | |
980 6 14 1 ; C12 - N8 | |
981 6 15 1 ; C12 - N9 | |
982 6 18 1 ; C12 - S18 | |
983 7 10 1 ; C13 - C16 | |
984 8 16 1 ; C14 - N11 | |
985 8 17 1 ; C14 - C17 | |
986 9 19 1 ; C15 - F19 | |
987 10 16 1 ; C16 - N11 | |
988 11 15 1 ; C4 - N9 | |
989 12 14 1 ; C5 - N8 | |
990 12 16 1 ; C5 - N11 | |
991 12 20 1 ; C5 - O20 | |
992 14 18 1 ; N8 - S18 | |
993 16 19 1 ; N11 - F19 | |
994 17 19 1 ; C17 - F19 | |
995 21 3 1 ; O21 - C3 | |
996 21 12 1 ; O21 - C5 | |
997 | |
998 [ angles ] | |
999 ; ai aj ak funct theta cth | |
1000 1 2 3 1 1.8000e+02 4.4183e+02 ; C1 - C2 - C3 | |
1001 1 13 12 1 1.8000e+02 4.6944e+02 ; C1 - C6 - C5 | |
1002 2 1 13 1 1.1532e+02 5.4476e+02 ; C2 - C1 - C6 | |
1003 2 1 21 1 1.2234e+02 5.8409e+02 ; C2 - C1 - O21 | |
1004 2 3 11 1 1.1558e+02 5.4266e+02 ; C2 - C3 - C4 | |
1005 2 3 20 1 1.2234e+02 5.8409e+02 ; C2 - C3 - O20 | |
1006 3 11 4 1 1.2269e+02 5.3220e+02 ; C3 - C4 - C7 | |
1007 3 11 12 1 1.1788e+02 5.4392e+02 ; C3 - C4 - C5 | |
1008 4 11 12 1 1.2591e+02 5.3388e+02 ; C7 - C4 - C5 | |
1009 4 14 15 1 1.0862e+02 6.1003e+02 ; C7 - N8 - N9 | |
1010 4 16 5 1 1.2049e+02 5.5815e+02 ; C7 - N11 - C10 | |
1011 4 16 6 1 1.0424e+02 5.9664e+02 ; C7 - N11 - C12 | |
1012 5 15 14 1 1.0834e+02 6.1505e+02 ; C10 - N9 - N8 | |
1013 5 16 6 1 1.2160e+02 5.8576e+02 ; C10 - N11 - C12 | |
1014 6 7 8 1 1.2000e+02 5.4894e+02 ; C12 - C13 - C14 | |
1015 6 7 19 1 1.1896e+02 5.6149e+02 ; C12 - C13 - F19 | |
1016 6 17 10 1 1.8000e+02 4.7447e+02 ; C12 - C17 - C16 | |
1017 7 6 16 1 1.2120e+02 5.8576e+02 ; C13 - C12 - N11 | |
1018 7 6 17 1 1.2000e+02 5.4894e+02 ; C13 - C12 - C17 | |
1019 7 8 9 1 1.8000e+02 4.7447e+02 ; C13 - C14 - C15 | |
1020 8 7 19 1 1.1875e+02 5.5274e+02 ; C14 - C13 - F19 | |
1021 8 9 10 1 1.8000e+02 5.3137e+02 ; C14 - C15 - C16 | |
1022 9 10 17 1 1.8000e+02 5.3137e+02 ; C15 - C16 - C17 | |
1023 11 3 20 1 1.2393e+02 5.7823e+02 ; C4 - C3 - O20 | |
1024 11 4 14 1 1.2198e+02 5.6568e+02 ; C4 - C7 - N8 | |
1025 11 4 16 1 1.2198e+02 5.6568e+02 ; C4 - C7 - N11 | |
1026 11 12 13 1 1.8000e+02 4.7447e+02 ; C4 - C5 - C6 | |
1027 13 1 21 1 1.2234e+02 5.8409e+02 ; C6 - C1 - O21 | |
1028 14 4 16 1 1.1390e+02 5.8576e+02 ; N8 - C7 - N11 | |
1029 15 5 16 1 1.1031e+02 6.1337e+02 ; N9 - C10 - N11 | |
1030 15 5 18 1 0.0000e+00 0.0000e+00 ; N9 - C10 - S18 | |
1031 16 5 18 1 0.0000e+00 0.0000e+00 ; N11 - C10 - S18 | |
1032 16 6 17 1 1.1687e+02 5.8241e+02 ; N11 - C12 - C17 | |
1033 | |
1034 [ dihedrals ] ; propers | |
1035 ; for gromacs 4.5 or higher, using funct 9 | |
1036 ; i j k l func phase kd pn | |
1037 1 2 3 11 9 180.00 0.00000 2 ; C1- C2- C3- C4 | |
1038 1 2 3 20 9 180.00 0.00000 2 ; C1- C2- C3- O20 | |
1039 1 13 12 11 9 180.00 0.00000 2 ; C1- C6- C5- C4 | |
1040 2 1 13 12 9 180.00 0.00000 2 ; C2- C1- C6- C5 | |
1041 2 3 11 4 9 180.00 12.02900 2 ; C2- C3- C4- C7 | |
1042 2 3 11 12 9 180.00 12.02900 2 ; C2- C3- C4- C5 | |
1043 3 11 4 14 9 180.00 16.73600 2 ; C3- C4- C7- N8 | |
1044 3 11 4 16 9 180.00 16.73600 2 ; C3- C4- C7- N11 | |
1045 3 11 12 13 9 180.00 0.00000 2 ; C3- C4- C5- C6 | |
1046 4 11 3 20 9 180.00 12.02900 2 ; C7- C4- C3- O20 | |
1047 4 11 12 13 9 180.00 0.00000 2 ; C7- C4- C5- C6 | |
1048 4 14 15 5 9 180.00 16.73600 2 ; C7- N8- N9- C10 | |
1049 4 16 5 15 9 180.00 6.06680 2 ; C7- N11- C10- N9 | |
1050 4 16 5 18 9 180.00 6.06680 2 ; C7- N11- C10- S18 | |
1051 4 16 6 7 9 180.00 7.74040 2 ; C7- N11- C12- C13 | |
1052 4 16 6 17 9 180.00 7.74040 2 ; C7- N11- C12- C17 | |
1053 5 16 4 11 9 180.00 7.11280 2 ; C10- N11- C7- C4 | |
1054 5 16 4 14 9 180.00 7.11280 2 ; C10- N11- C7- N8 | |
1055 5 16 6 7 9 180.00 7.74040 2 ; C10- N11- C12- C13 | |
1056 5 16 6 17 9 180.00 7.74040 2 ; C10- N11- C12- C17 | |
1057 6 7 8 9 9 180.00 0.00000 2 ; C12- C13- C14- C15 | |
1058 6 16 4 11 9 180.00 7.11280 2 ; C12- N11- C7- C4 | |
1059 6 16 4 14 9 180.00 7.11280 2 ; C12- N11- C7- N8 | |
1060 6 16 5 15 9 180.00 6.06680 2 ; C12- N11- C10- N9 | |
1061 6 16 5 18 9 180.00 6.06680 2 ; C12- N11- C10- S18 | |
1062 6 17 10 9 9 180.00 0.00000 2 ; C12- C17- C16- C15 | |
1063 7 6 17 10 9 180.00 0.00000 2 ; C13- C12- C17- C16 | |
1064 7 8 9 10 9 180.00 0.00000 2 ; C13- C14- C15- C16 | |
1065 8 7 6 16 9 180.00 27.82360 2 ; C14- C13- C12- N11 | |
1066 8 7 6 17 9 180.00 27.82360 2 ; C14- C13- C12- C17 | |
1067 8 9 10 17 9 180.00 0.00000 2 ; C14- C15- C16- C17 | |
1068 9 8 7 19 9 180.00 0.00000 2 ; C15- C14- C13- F19 | |
1069 10 17 6 16 9 180.00 0.00000 2 ; C16- C17- C12- N11 | |
1070 11 4 14 15 9 180.00 41.84000 2 ; C4- C7- N8- N9 | |
1071 12 11 3 20 9 180.00 12.02900 2 ; C5- C4- C3- O20 | |
1072 12 11 4 14 9 180.00 16.73600 2 ; C5- C4- C7- N8 | |
1073 12 11 4 16 9 180.00 16.73600 2 ; C5- C4- C7- N11 | |
1074 13 1 2 3 9 180.00 0.00000 2 ; C6- C1- C2- C3 | |
1075 14 15 5 16 9 180.00 16.73600 2 ; N8- N9- C10- N11 | |
1076 14 15 5 18 9 180.00 16.73600 2 ; N8- N9- C10- S18 | |
1077 15 14 4 16 9 180.00 41.84000 2 ; N9- N8- C7- N11 | |
1078 16 6 7 19 9 180.00 27.82360 2 ; N11- C12- C13- F19 | |
1079 17 6 7 19 9 180.00 27.82360 2 ; C17- C12- C13- F19 | |
1080 21 1 2 3 9 180.00 0.00000 2 ; O21- C1- C2- C3 | |
1081 21 1 13 12 9 180.00 0.00000 2 ; O21- C1- C6- C5 | |
1082 | |
1083 [ dihedrals ] ; impropers | |
1084 ; treated as propers in GROMACS to use correct AMBER analytical function | |
1085 ; i j k l func phase kd pn | |
1086 3 4 11 12 4 180.00 4.60240 2 ; C3- C7- C4- C5 | |
1087 5 4 16 6 4 180.00 4.60240 2 ; C10- C7- N11- C12 | |
1088 6 8 7 19 4 180.00 4.60240 2 ; C12- C14- C13- F19 | |
1089 7 17 6 16 4 180.00 4.60240 2 ; C13- C17- C12- N11 | |
1090 11 2 3 20 4 180.00 43.93200 2 ; C4- C2- C3- O20 | |
1091 11 16 4 14 4 180.00 4.60240 2 ; C4- N11- C7- N8 | |
1092 18 16 5 15 4 180.00 4.60240 2 ; S18- N11- C10- N9 | |
1093 21 1 13 2 4 180.00 43.93200 2 ; O21- C1- C6- C2 | |
1094 | |
1095 ; Include water topology | |
1096 #include "oplsaa.ff/spce.itp" | |
1097 | |
1098 #ifdef POSRES_WATER | |
1099 ; Position restraint for each water oxygen | |
1100 [ position_restraints ] | |
1101 ; i funct fcx fcy fcz | |
1102 1 1 1000 1000 1000 | |
1103 #endif | |
1104 | |
1105 ; Include topology for ions | |
1106 #include "oplsaa.ff/ions.itp" | |
1107 | |
1108 [ system ] | |
1109 ; Name | |
1110 TEST | |
1111 | |
1112 [ molecules ] | |
1113 ; Compound #mols | |
1114 Protein 1 | |
1115 base 1 |